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FunChIP

This is the development version of FunChIP; for the stable release version, see FunChIP.

Clustering and Alignment of ChIP-Seq peaks based on their shapes


Bioconductor version: Development (3.19)

Preprocessing and smoothing of ChIP-Seq peaks and efficient implementation of the k-mean alignment algorithm to classify them.

Author: Alice Parodi [aut, cre], Marco Morelli [aut, cre], Laura M. Sangalli [aut], Piercesare Secchi [aut], Simone Vantini [aut]

Maintainer: Alice Parodi <alicecarla.parodi at polimi.it>

Citation (from within R, enter citation("FunChIP")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("FunChIP")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("FunChIP")
An introduction to FunChIP PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, Clustering, Software, StatisticalMethod
Version 1.29.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License Artistic-2.0
Depends R (>= 3.5.0), GenomicRanges
Imports shiny, fda, doParallel, GenomicAlignments, Rcpp, methods, foreach, parallel, GenomeInfoDb, Rsamtools, grDevices, graphics, stats, RColorBrewer
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package FunChIP_1.29.0.tar.gz
Windows Binary FunChIP_1.29.0.zip
macOS Binary (x86_64) FunChIP_1.29.0.tgz
macOS Binary (arm64) FunChIP_1.29.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/FunChIP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/FunChIP
Bioc Package Browser https://code.bioconductor.org/browse/FunChIP/
Package Short Url https://bioconductor.org/packages/FunChIP/
Package Downloads Report Download Stats